Hoffman2:Interactive Sessions

Back to all things Hoffman2

Interactive sessions on Hoffman2 let you have access to a computing node for up to 24 hours. This is ideal for:

• running a intensive program like MATLAB (in fact that's how it works), WEKA, R or FSLView
• debugging a script you will be submitting to the queue later
• moving/tar'ing/untar'ing lots of files
• any other computing or graphics intensive operations

since you aren't supposed to use the login nodes for such heavy lifting.

Basic Command

To get one, you need to use the qrsh command with the -l i flag.

For example

$ qrsh -l i

will try to get you an interactive node. That dash-elle flag followed by the "i" is specifying that you want an interactive resource.

Because you didn't specify a time limit this session will only last two hours after which you will be kicked off of the interactive node back to a login node.

And because you didn't specify a memory limit, as of September 2013 job memory enforcement is strict so you will be kicked off if you cross ATS's default memory limit. As of 2013.09.09 this default was 1GB.

And if all the interactive nodes are busy (there are only so many of them), then you will be told it was unable to secure one for you.

If you successfully get a node, your prompt will change from something like

[joebruin@login4 ~] $

to something like

[joebruin@n1234 ~] $

indicating you are on node 1234.

Longer Time

If you wanted to specify a a time limit for your interactive session (anything less than 24 hours), use the resource flag again and specify time in the HH:MM:SS format.

For example

$ qrsh -l i,h_rt=4:00:00

will try securing an interactive node for four hours with the default amount of RAM, but if they are all taken you will be kindly told you are out of luck.

More Memory

Doing something memory intensive? Like working with a lot of visualizations or multiple datasets? Use the resource flag again and specify a data request.

For example

$ qrsh -l i,h_rt=4:00:00,h_data=4G

will try securing an interactive node for four hours with four gigabytes of RAM, but if no such node is available the cluster will deny your request.

Tips

Sometimes inactivity on your computer will result in Hoffman2 connection break [ Broken Pipe ] (even while computing).

To prevent this from happening: For Macs - in your /etc/ssh_config -add this line to the bottom

ServerAliveInterval 180

This will tell your ssh to ping the server every 180 seconds to prevent it from timing out.

External Links

• Getting an interactive node