Interactive Command-Line Sessions on Compute Nodes

Posted on
Updated on

November 21, 2023

When testing software and writing job submission scripts for the cluster we recommend using an interactive session or working on an Scientific Computing (SciC) Linux Clusters Virtual Desktop. Problems show up quicker when working interactively rather than waiting for a batch job to finish.

Interactive session - without graphics

  • Estimate the memory requirements (in MB) and number of parallel processor threads that will run in the session
  • Once on erisone.partners.org, use 'bsub' to start the session with the desired resource reservation (eg. for 10000MB RAM and 4 CPU threads):
bsub -Is -R 'rusage[mem=10000]' -n 4 /bin/bash

Interactive session - with X11 graphics

  • To export X11 graphics from the cluster to your computer an X11 display must be running on your computer
    • Linux: no additional steps need to be taken
    • Mac: Install the latest version of XQuartz 
    • Windows: There are various X11 applications for Windows, however the installation details are outside the scope of this document.  The SciC Linux Clusters Virtual Desktop is a more user friendly alternative to X11 forwarding on Windows.
  • Login to SciC Linux Clusters over SSH with X11 forwarding:
ssh -X username@erisone.partners.org 
  • Estimate the memory requirements (in MB) and number of parallel processor threads that will run in the session
  • Use 'bsub' with the '-XF' parameter to start the session with the desired resource reservation (eg. for 10000MB RAM and 4 CPU threads):
bsub -XF -R 'rusage[mem=10000]' -n 4 -Is /bin/bash
Job <362588> is submitted to default queue <interact>.
<<ssh X11 forwarding job>>
<<Waiting for dispatch ...>>
<<Starting on cmu054>>

 

Advanced options

Specific host groups can be requested using the -m parameter to bsub

Go to KB0027950 in the IS Service Desk

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