Normally when you call
qsub PBS grabs your script and goes
away. You get the prompt returned to you almost immediately and whatever
output is produced from your job goes into a designated file. But
what if you want to run an interactive job, e.g., a matlab session?
This is not, in general, the right way to use supercomputers, because
interactive jobs waste enormous amount of CPU time, mostly because
humans are so slow. Even if you could type 1000 characters per second,
you would still waste enormous amount of CPU time, because computers
can easily type 500,000,000 characters per second or more (and
high end graphic displays, the so called frame buffers, can display
the characters this fast, but only as pixels).
The way to run such an interactive job is to call
qsub -I. The
-I option will make PBS
arrange for an interactive login
session on an available AVIDD node and your TTY will be reconnected to
that session. On exiting the session you'll get back to the original
TTY. Here is how it works:
[gustav@bh1 gustav]$ hostname bh1 [gustav@bh1 gustav]$ pwd /N/B/gustav [gustav@bh1 gustav]$ qsub -I qsub: waiting for job 12529.bh1.avidd.iu.edu to start qsub: job 12529.bh1.avidd.iu.edu ready [gustav@bc55 gustav]$ hostname bc55 [gustav@bc55 gustav]$ pwd /N/B/gustav [gustav@bc55 gustav]$ exit qsub: job 12529.bh1.avidd.iu.edu completed [gustav@bh1 gustav]$I start from the head node, bh1, and request an interactive session. PBS takes my request, assigns it a job ID of 12529.bh1, and then gives me a shell on bc55. On exiting the shell on bc55 the PBS job terminates and I get back to the head node, bh1.
The computational nodes of the AVIDD cluster are configured for computation
only. They have no X11 installed on them. This means that you cannot
run any X11 tools on those nodes and you cannot even run emacs there,
which is a pity, because emacs can be used as a computational tool. It
is, after all, a Lisp machine emulator. But you can compile and run
your own X11 program on computational nodes, because they have the
full X11 library installed, and you can compile and run your own emacs
too. And you can copy an existing X11 binary from /usr/X11R6/bin to
When you run X11 tools on computational nodes, the traffic is routed through bh3.uits.indiana.edu (on avidd-b), so that you should either add bh3.uits.indiana.edu to the list of hosts allowed to display windows on your X11 server, or - a better practice - use Xauthority.
Here is a simple example that shows how to do this:
[gustav@bh1 gustav]$ cp /usr/X11R6/bin/xclock bin/xclock [gustav@bh1 gustav]$ cp /usr/X11R6/bin/xterm bin/xterm [gustav@bh1 gustav]$ qsub -I qsub: waiting for job 12546.bh1.avidd.iu.edu to start qsub: job 12546.bh1.avidd.iu.edu ready [gustav@bc55 gustav]$ export DISPLAY=woodlands.tqc.iu.edu:0.0 [gustav@bc55 gustav]$ xclock &  5709 [gustav@bc55 gustav]$ xterm &  5710 [gustav@bc55 gustav]$ exit qsub: job 12546.bh1.avidd.iu.edu completed [gustav@bh1 gustav]$
Since you have copied xterm to your private bin already, you can get yourself
a more functional interactive window on a computational node simply
by submitting a script, which calls xterm, without the
Here is the example of the script:
[gustav@bh1 PBS]$ cat xterm.sh #!/bin/bash xterm -display woodlands.tqc.iu.edu:0.0 exit 0 [gustav@bh1 PBS]$ qsub xterm.sh 12550.bh1.avidd.iu.edu [gustav@bh1 PBS]$Submitting the script to PBS will produce, after a short while, an xterm window running on a PBS allocated node on your X11 server. Exiting the shell in the window terminates the job.