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Submitting Jobs - Interactive Submission

Without GUI(Graphical User Interface)

When logged on, users can execute the slurm srun command to get an interactive bash terminal with almost all the same commands as the normal login terminal:

srun -c [CoresPerNode] -N [NumberOfNodes] -p [Partition] --pty /bin/bash

The commands can be executed in parallel, provided you use MPI (via mpirun command) or background tasks (via bash job control):

Skip Example

[jspngler@log001 extended]$ srun -c 2 -N 5 -p computeq --pty /bin/bash
srun: job 70942 queued and waiting for resources
srun: job 70942 has been allocated resources
[jspngler@c064 extended]$ squeue -j 70942
         JOBID PARTITION NAME     USER ST TIME NODES NODELIST(REASON)
         70942  computeq bash jspngler  R 1:07     5       c[064-068]
[jspngler@c064 extended]$ hostname
c064
[jspngler@c064 extended]$ module load openmpi/3.1.1/gcc.8.2.0
[jspngler@c064 extended]$ mpirun hostname
c066
c064
c065
c067
c068
[jspngler@c064 extended]$ for i in 'scontrol show hostnames $SLURM_NODELIST'
> do ssh $i hostname 
> done &
[1] 94485
c064
c065
c066
c067
c068
[jspngler@c064 extended]$ jobs
[1]+ Done for i in 'scontrol show hostnames $SLURM_NODELIST';
do
ssh $i hostname;
done
[jspngler@c064 extended]$

With GUI

You can start an interactive job with x11 option/switch to enable graphics:

srun --x11 -c 2 xterm

Starting an application directly is possible too:

srun --x11 -c 2 /public/apps/matlab/R2018a/bin/matlab

In order to take advantage of the cluster's GUI interactivity, users need an X windows server and a terminal with X windows capability installed. In Linux and MacOS X, the X server is already present. Windows users must install an X Server that works with putty or cygwin. MacOS X and Linux users must use a terminal with X Windows capability. Remember that your uuid is the same as the one you use in myMemphis.

Windows

Putty with Xming or CygWin/MobaXTerm will provide an X windows environment for GUI capability.

Putty with Xming

  1. Install Putty and Xming
  2. start Xming from the start menu or shortcut
  3. Open Putty
  4. Fill in "Hostname" box normally (with uuid@hpclogin.memphis.edu)
  5. Left click or tab and arrow down to Connection->SSH->X11 via "Category" menu on left
  6. Check "Enable X11 forwarding" box
  7. Fill in "X display location" box with localhost:0.0
    1. 0.0 may be different if you have multiple X windows servers running
    2. hover mouse over Xming icon on the taskbar notification area to see which one is needed
  8. Left click or tab to "Open" button to start session

MobaXTerm

  1. Download stand-alone and extract or installer and install
  2. Open MobaXTerm
  3. Left click X server icon (top right) if it isn't started (hover mouse over X server icon to check status of X server)
  4. Open local terminal
  5. Type ssh -Y uuid@hpclogin.memphis.edu and press enter on keyboard

CygWin

  1. Install CygWin with packages
    1. Xorg-Server
    2. X11
    3. OpenSSH
  2. Open CygWin Terminal
  3. Type startxwin and press enter on keyboard
  4. Go to taskbar notification area and left click or tab to CygWin Apps->System Tools->XTerm
  5. Left click or enter to start XTerm
  6. Type ssh -Y uuid@hpclogin.memphis.edu and press enter on keyboard

Linux

Almost every version of linux provides an X11 capable terminal emulator. If you can't find one, consult your distribution's documentation or contact us. Open up an X11 terminal (might be called terminal, console, XTerm, konsole, etc...) and type ssh -Y uuid@hpclogin.memphis.edu and press enter on keyboard.

Mac OS X

Although Mac OS X is based on Darwin, a Linux like OS with many similar features and programs, an X windows capable terminal is not installed by default. Install X Quartz to get an X windows capable terminal, but keep in mind that newer versions of X Quartz don't seem to work over remote terminal.

  1. Install X Quartz 2.7.8
  2. Open X Quartz Terminal
  3. Type ssh -Y uuid@hpclogin.memphis.edu and press enter on keyboard

x2go

The x2go client application, which gives a full desktop and better connection compression on a login node, can be installed on Windows, OS X, and linux. It can be downloaded here. Once installed, create a new session with the following settings:

  • Host: "hpclogin.memphis.edu" (alternatively, you can use "hpc18login1.memphis.edu" or "hpc18login2.memphis.edu" for persistent sessions)
  • Login: Your uuid
  • SSH Port: "22"
  • Session Type: "XFCE"

Then save the session, and click  on the session from the main application screen where you will be prompted for your password to connect. Once on the desktop, you can open a terminal from the bottom bar of the screen. To run srun --x11 ... interactive jobs, you should try the following sequence (otherwise you get an error about forwarding x11 over srun):

ssh log002 -Y
srun --x11 -c 2 xterm