3.4 Interactive batch jobs

Interactive batch jobs can be used in Taito for running graphical interfaces or other tasks that require input from the user during the execution of the computing task. Note, that you may need to queue for SLURM to allocate these resources, except if you choose Taito-shell, see below.

The most easy way to run interactive batch jobs is to use Taito-shell, described in chapter 8 of this guide. When a taito-shell session is opened, the session is actually an interactive batch job, that has following properties:

  • Unlimited running time
  • Computing capacity up to 4 cores per session
  • Shared memory of up to 128 GB per session
You can open Taito-shell session, either by directly connecting taito-shell.csc.fi:
ssh -X taito-shell.csc.fi -l csc_user_id
or if you have already logged in to Taito, you can open a Taito-shell session with command:
sinteractive

 

In cases, the you can't use taito-shell/sinteractive ( e.g. in the case of interactive mpi jobs), you can use the srun command to launch interactive batch job sessions. For example command:

 srun -n1 -t02:00:00 --x11=first --pty $SHELL

would launch interactive batch jobs session, running the default command shell ( $SHELL). In the command above, one core (-n1 ) is reserved for two hours (-t02:00:00). The definition --x11=first sets up the x11 connection so that graphical user interfaces can be used.

Bellow is a sample session where the VMD molecular visualization program is started on an interactive batch job session. Note that after the srun command, the commands are not executed in the login node any more. In stead the VMD is now started in one of the computing nodes ( node c120 in this case ) and thus VMD is not causing extra load to the login node:

[kkayttaj@taito-login4 kkayttaj]$ srun -n1 -t02:00:00 --x11=first --pty $SHELL
[kkayttaj@c120 kkayttaj]$ module load vmd
VMD version 1.9.1 is now in use
[kkayttaj@c120 kkayttaj]$ vmd

You can also use interactive batch job sessions to test your software. In these cases you can use srun as above or alternatively, first the resource allocation with command: salloc and the submit jobs with srun command.

In the example bellow a request for 32 cores (-n 32) with 1 GB/core (--mem-per-cpu=1000) for 30 minutes (-t00:30:00)  is submitted with the salloc command. Two full Taito Sandy Bridge (--constraint=snb) nodes nodes will be reserved for the interactive job as 16 cores will be used from one node ( --ntasks-per-node=16). Once the resource allocation is done the Gromacs jobs can be launched using the srun command:

salloc -n 32 --ntasks-per-node=16 --constraint=snb --mem-per-cpu=1000 -t00:30:00 -p parallel
srun mdrun_mpi -s topol1 -dlb yes
srun mdrun_mpi -s topol2 -dlb yes
exit

In the example above the exit command closes the resource allocation done by the salloc command.

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