Editing Scanco Administration (section)

====Running long calculations====

Here are some useful tips for running long jobs.

=====Getting the prompt back after starting a job=====

Use & at the end of the command. This puts the job in the background. For example:

 ./myjob someargs &

To see all your background jobs (the ones started in the current shell), enter:

 jobs

To bring one of these to the foreground, use:

 fg %n

where <tt>n</tt> is the job number (yes it needs a <tt>%</tt> in front of it). To move it to the background again, hit CTRL-Z. This however doesn't just move the job to the background, it suspends it. To get it running again, use

 bg %n


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=====Keeping a job running after you log out=====

Use nohup. For example, suppose you want to run <tt>./myjob 20</tt>. In this case, you could use:

 nohup nice ./myjob 20 &> output &

There are several things to note here:

* The <tt>&</tt> at the end of the command line is there so you get the command prompt back immediately (see the previous section).
* We have redirected the output to a file out_file with <tt>&> output</tt>. If you don't do this, any output to STDIN (normally the console) will automatically go into a file called <tt>nohup.out</tt>.
* We've niced the job to reduce it's execution priority. This is courteous if you're a multiuser system. 

If you want to see what's in nohup.out (or whatever you called it) at any time, you can do the usual

 cat nohup.out

Here's another potentially more useful command:

 tail -f nohup.out

tail shows you the last few lines of the files. In addition, the -f flag ("follow") means that as lines get added to the file, they are displayed on the screen. This looks just like when you run the program without nohup, except when you hit CTRL-C, the program keeps on running in the background.


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=====Finding out if any of your jobs are still running=====

This command will show all jobs that belong to user "eric":

 ps -u eric

Another useful command is "top", which will show interactively which processes are using the most processor cycles.


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=====Terminating a job prematurely=====

If you decide that you want to kill the job before it completes, this is the command:

 kill PID

where PID is the actual PID (a number) of the process.  You find the PID with 'top' or 'ps -u eric'  (replace eric by your user ID of course).

Occasionally a process will decline to terminate when you request it to.  This is the more brutal, never-fails method to kill a job immediately:

 kill -s KILL PID


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=====Suspending a long-running job and restarting it later=====

First find the PID (process ID) with top or with ps. For example, I might list all jobs belonging to me with:

 ps -u eric

To stop the job, send it a STOP signal:

 kill -s STOP PID

(replace PID with the actual PID number). It is now no longer running, but it still occupies memory (although the memory it uses will probably be swapped out to disk). When you want to resume execution, give it a CONT signal:

 kill -s CONT PID


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