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Managing Jobs on LINCOMM
One of the main reasons for using LINCOMM is that it can run very long jobs. This article will teach you how to manage such jobs on LINCOMM.
taken from SSCC's Linstat KB
Foreground and Background Jobs
Normally when you type a command, it is processed and you see the results (if any) before the cursor returns and you can type a new command. These jobs are said to be running in the foreground. If you put a job in the background, the cursor returns immediately and you can keep giving commands and doing other work while the your job is running. When the job finishes a message will appear on your screen.
If a job is running in the background it will keep running even if you log out, so you can start a long job before you leave in the evening, log out, and get the results the next morning (or next week, or next month). Just keep track of which LINCOMM server you are using when you start a job, because if you need to manage that job you'll need to return to that server.
What you should not do when you have a job running in the background is start another CPU-intensive job
To run a job in the background, add an ampersand ( & ) at the end of the command. For example, if you type:
stata -b do myprogram
Stata will start and run myprogram.do in the foreground. Thus your session will be unavailable until the job is done. On the other hand:
stata -b do myprogram &
runs Stata in the background. The cursor returns immediately and you can do other things while Stata is running your program. When it is done you'll see a message like:
 Done stata -b do myprogram
If you have a job running in the foreground and want to put it in the background, press CTRL-z (if the job has opened a separate window, you must return to your main LINCOMM window before pressing CTRL-z ). The current job will be suspended and you will get your cursor back. Then type bg to put it in the background—it will not run while suspended. You can also type fg to move it back to the foreground, either from being suspended or from the background.
The ps command (think processes) gives you a list of processes you are running on the server. The output will be similar to the following:
PID TTY TIME CMD 29413 pts/30 00:00:00 tcsh 1601 pts/30 00:00:00 emacs 1602 pts/30 00:00:00 emacs 1605 pts/30 00:00:00 ps
PID is short for Process IDentifier, and is used when you need to specify a particular job. Keep in mind that LICNOMM is a cluster of four servers, and ps will only show you the jobs you are running on the server you're logged into. See Switching Between LINCOMM Servers to learn how to get back to the LINCOMM server where you started your job.
Unfortunately, the default ps output will only show jobs you started in your current session. To see all your jobs from any session, type:
ps aux | grep NetID
where NetID should be replaced by your NetID (e.g. ps aux | grep jdoe ). This lists all jobs on the server, then filters it to only show yours.
Another useful command for monitoring jobs is top . This will tell you the "top" jobs (in terms of resources used) currently running on the server. With it you can verify that your job is actually doing work by checking that its %CPU is greater than zero, though jobs can easily get stuck in a state where they use CPU without doing anything productive.
top also gives you a sense of how busy the server is. The LINCOMM servers have 24 CPUs, so if %CPU adds up to more than 2400% programs will have to share the available CPU time. If the LINCOMM you're on has less CPU time available than your program is capable of using, consider switching to a different LINCOMM.
Unfortunately top does not monitor all the resources a server needs to run jobs.
If you need to stop a running job, use the kill command. Simply type kill and then the PID of the job you want to kill. For example:
This doesn't actually stop the job, it merely requests that it shut down, giving the program an opportunity to clean up temporary files and such. On the other hand, adding the -9 switch to the kill command will kill a program immediately with or without its consent. Thus:
kill -9 1602
will kill process 1602.
LINCOMM is actually a cluster of four servers. When you log in you're assigned to a server randomly to try to balance the load between them. However, you can choose to connect to a specific server to monitor a job you started previously or if the server you're assigned to turns out to be particularly busy.
Be sure to note which server you're on when you start a long job. If the server name is not in your prompt, you can identify it by typing: