Interactive jobs

Sometimes you might want to test or debug a calculation interactively, but running interactively on the login node is discouraged and not an option.

Asking for an interactive job

Instead of running on a login node, you can ask the queue system to allocate compute resources for you and once assigned, you can run commands interactively for as long as requested. The examples below are for devel jobs, but the procedure also holds for the other job types except optimist jobs.

On Fram and Betzy:

$ srun --nodes=1 --time=00:30:00 --qos=devel --account=YourAccount --pty bash -i

On Saga:

$ srun --ntasks=1 --mem-per-cpu=4G --time=00:30:00 --qos=devel --account=YourAccount --pty bash -i

When you are done, simply exit the shell (exit, logout or ^D) to end the job.

The arguments between srun and --pty could be any arguments you would have given to sbatch when submitting a non-interactive job. However, --qos=devel is probably a good idea to avoid waiting too long in the queue.

Note that interactive jobs stop when you log out from the login machine, so unless you have very long days in office (or elsewhere, for that matter), specifying more than 6-8 hrs runtime is not very useful. An alternative is to start the job in a tmux session (next section).

Keeping interactive jobs alive

Interactive jobs stop when you disconnect from the login node either by choice or by internet connection problems. To keep a job alive you can use a terminal multiplexer like tmux.

tmux allows you to run processes as usual in your standard bash shell

You start tmux on the login node before you get a interactive Slurm session with srun and then do all the work in it. In case of a disconnect you simply reconnect to the login node and attach to the tmux session again by typing:

$ tmux attach

Or in case you have multiple session running:

$ tmux list-session
$ tmux attach -t SESSION_NUMBER

As long as the tmux session is not closed or terminated (e.g. by a server restart) your session should continue. One problem with our systems is that the tmux session is bound to the particular login server you get connected to. So if you start a tmux session on login-1 on SAGA and next time you get randomly connected to login-2 you first have to connect to login-1 again by:

$ ssh login-1

To log out a tmux session without closing it you have to press Ctrl-B (that the Ctrl key and simultaneously “b”, which is the standard tmux prefix) and then “d” (without the quotation marks). To close a session just close the bash session with either Ctrl-D or type exit. You can get a list of all tmux commands by Ctrl-B and the ? (question mark). See also this page for a short tutorial of tmux. Otherwise working inside of a tmux session is almost the same as a normal bash session.

Graphical user interfaces in interactive jobs

It is possible to run X commands, i.e., programs with a graphical user interface (GUI), in interactive jobs. This allows you to get graphical output back from your job running on a login node. (Note that currently, this has not been activated on Betzy.)

First, you must make sure that you have turned on X forwarding when logging in to the cluster. With ssh from a Linux or MacOS machine, you do this with the -Y flag, e.g.:

$ ssh -Y fram.sigma2.no

or:

$ ssh -Y saga.sigma2.no

Check that the X forwarding works by running a graphical command like emacs & and verify that it sets up a window. (Note that due to network latency, it can take a long time to set up a window.)

To be able to run X commands in interactive jobs, add the argument --x11 (note the lowercase x) to srun, like this:

On Fram:

$ srun --nodes=1 --time=00:30:00 --qos=devel --account=YourAccount --x11 --pty bash -i

On Saga:

$ srun --ntasks=1 --mem-per-cpu=4G --time=00:30:00 --qos=devel --account=YourAccount --x11 --pty bash -i

The difference between salloc and srun

An alternative to using srun ... --pty bash -i is to use

$ salloc --nodes=1 --time=00:30:00 --qos=devel --account=YourAccount

And equivalently on Saga.

As with srun, the arguments to salloc can be any you would have given to sbatch. salloc will also give you an interactive shell, but note that the shell will be running on the login node. That means that you must start all calculations with srun or mpirun or equivalent, to make sure they run on the allocated compute node(s). For this reason, the srun method is probably preferable in most cases (it also works more like a batch job). However, there might be situations when the srun method doesn’t work properly, in which case you can try with salloc.

With this method, you can run X commands without adding any switch to the salloc command, but note again that the commands will be run on the login node. In some cases, this is what you want (see for instance TotalView).