qlogin

The simplest thing you can do with the cluster is to just log in to the BIOSTAT node and run things on it interactively (an even simpler option might be to use IDAS). Once you’re logged in, it is just like being logged in remotely to any other computer. However, logging in must be accomplished through the scheduler to balance requests for interactive and non-interactive sessions and to send requests to the proper queues. To set up an interactive session, use qlogin:

qlogin -q BIOSTAT -pe smp 1

An explanation of the arguments:

-q BIOSTAT: Log in to the BIOSTAT node. You can, of course, try to log in interactively to a different node with, say -q UI or -q all.q.
-pe smp 1: Request an interactive session with a single core. To request, say, 4 cores, you would use -pe smp 4. The option stands for “parallel environment: symmetric multiprocessing”, if you are curious.

Warning: If you omit -pe smp <number>, qlogin will allocate all of the available processors on the node to your qlogin request. In other words, you may be requesting dozens of processors that no one else will be able to use until you log out (which you would do by typing exit or Ctrl+D). This is particularly bad if you only need a small number of processors, or if you intend to stay logged in for a long period of time (or both!).

From here, you can do anything you would normally do at a terminal – run commands, run an interactive R session, etc. There are three primary reasons one might be interested in doing this:

Your own computer has insufficient computational resources to run the interactive R session you have in mind.
You need to set something up on the cluster, but don’t want to tie up a login node.
You want to make sure a job will run on Argon or troubleshoot why it isn’t running (it can be difficult to do this non-interactively).

Reminder: Try not to abuse qlogin by staying logged in for long periods of time or requesting far more slots than you are actually going to use. This ties up resources that other people may be trying to use.

Requesting a specific node

You can request that your qlogin command takes you to a specific type of machine by including various logical flags. For example, to specify that you need to log in to the high memory (384GB) node:

qlogin -q BIOSTAT -pe smp 4 -l mem_384G=true

Similarly, if you want to specifically request the lower-memory node for some reason:

qlogin -q BIOSTAT -pe smp 4 -l mem_128G=true

See here for the full list of flags that one can specify. Note that these flags are much more important on the UI and all.q queues, since there is a far greater variety of machines on those queues than on BIOSTAT. In particular, you might be interested in the -l gpu=TRUE flag if you want to run something on a GPU (there are no GPU machines on the BIOSTAT queue at this time).

All of these flags (-q, -pe, -l) also apply to jobs submitted with qsub, which we discuss next.