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Summary

Next steps

  • Q/A session
  • Exercises for the interested.

Today's topics

  • Overview of UPPMAX systems

    • NAISS-SENS

    • Several clusters, like

      • Bianca
      • Rackham

    • Login and compute nodes

  • Legal and administrative aspects

    • Sensitive personal data
    • Pseudonymisation and anonymisation
    • Apply for project

  • Logging in

    • ThinLinc, a must for graphics
    • ssh, may be faster if you just use command-line
    • VPN
    • 2FA

  • Command-line intro

    • navigation, using cd
    • file and directory management
    • change file permission, using chmod

  • Module system and workflows

    • modules adds paths to tools

      • module load ...
      • bioinfo-tools may be required to load you tool

    • workflows

  • Transferring files

    • The wharf works like a dock at the harbour.

    • There are several ways to use the wharf to transfer files

    • copy

    • transit server
    • rsync, scp/sftp

  • Introduction to compute nodes

    • Submitting jobs

      • Slurm, sbatch, the job queue
      • Jobs
      • Slurm parameters

      • Interactive jobs

        • allows you to work interactively with command line and your tools but on a compute node.

    • Other Slurm tools

    • Summary about the Bianca Hardware