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10-interactive.md

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title teaching exercises
Interactive Slurm Jobs
10
0

:::::::::::::::::::::::::::::::::::::: questions

  • How to start and exit an interactive Slurm job?

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::::::::::::::::::::::::::::::::::::: objectives

  • Explain how to use salloc to run interactive jobs

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Interactive jobs

Up to this point, we've focused on running jobs in batch mode. There are frequently tasks that need to be done interactively. Creating an entire job script might be overkill, but the amount of resources required is too much for a login node to handle. To solve this, Slurm provides the ability to start an interactive session.

Interactive sessions are commonly used for:

  • Data management, eg. organising files, truncation and recall of files, downloading datasets.
  • Software/workflow preparation/testing, eg. developing/debugging scripts, downloading/building software.
  • Interactive data analysis.
  • Rapid analysis cycles.
  • Running n application with a GUI.

On Milton, you can easily start an interactive job with salloc.

salloc --time 1:00:00 --cpus-per-task 1 --mem 1G  -p interactive

salloc command example

You will be presented with a bash prompt. Note that the prompt will change to reflect your new location (sml-n02 in the example), which is the compute node we are logged onto. You can also verify this with hostname.

Remember that, you may have to wait for resources, depending on the status of the queue you are requesting. We have designed the interactive partition to provide high availability, but only one job per user.

The interactive job will be cancelled and removed from the queue, if your terminal session is terminated or closed, and/or internet connection is lost (connection with the slurm node lost). It is recommended to use screen or tmux

When you have finished your task, please remember to close the session using exit or Ctrl-D.

You can also cancel the session using scancel.

If you need more resources you can run interactive sessions in the other partitions.

::: callout

These instructions are specific Milton!

salloc is setup slightly differently to its default behaviour. Not all HPC facilities have Slurm to start interactive jobs like in Milton! Be aware of this when using the command at other facilities.

:::::::::::

Creating remote graphics

To see graphical output inside your jobs, you need to use X11 forwarding. To connect with this feature enabled, use the -Y option when you login to the login nodes or vc7-shared.

ssh -Y vc7-shared

To use it in an interactive session add it to --x11 to your salloc command

salloc --time 1:00:00 --cpus-per-task 1 --mem 1G  -p interactive --x11
salloc: Pending job allocation 11803274
salloc: job 11803274 queued and waiting for resources
salloc: job 11803274 has been allocated resources
salloc: Granted job allocation 11803274
salloc: Nodes sml-n03 are ready for job

module load relion
Loading Relion 3.1.3 using CUDA 11.2
Using MotionCor2 1.5.0 at /stornext/System/data/nvidia/motioncor2/motioncor2-1.5.0cu11.2/bin/motioncor2
No matching version of Gctf exists for CUDA 11.2
Using CTFFIND 4.1.14 at /stornext/System/data/nvidia/ctffind/ctffind-4.1.14/bin/ctffind

        WARNING: verify that the area where Relion will be used
        is not over its storage quota. If Relion is unable to write
        files this might cause severe corruption in the Relion
        pipeline star files.


Loading relion/3.1.3-cu11.2
  Loading requirement: cuda/11.2 mpich-slurm/3.4.2

relion

We will now have a live demo for more interactive options on Milton.

::::::::::::::::::::::::::::::::::::: keypoints

  • Use salloc to start a new interactive Slurm job on Milton.
  • Use --x11 with salloc to run remote graphics in your interactive job.

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